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Proc Biol Sci. 2016 Aug 31;283(1837). pii: 20161200. doi: 10.1098/rspb.2016.1200.

Using viromes to predict novel immune proteins in non-model organisms.

Author information

1
Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego 92182, USA steven.quistad@gmail.com.
2
Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego 92182, USA.
3
Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego 92182, USA.
4
Center for Microbial Oceanography: Research and Education, Department of Oceanography and Sea Grant College Program, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, HI 96822, USA.
5
Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego 92182, USA Computational Science Research Center, San Diego State University, 5500 Campanile Drive, San Diego 92182, USA Department of Computer Science, San Diego State University, 5500 Campanile Drive, San Diego 92182, USA.

Abstract

Immunity is mostly studied in a few model organisms, leaving the majority of immune systems on the planet unexplored. To characterize the immune systems of non-model organisms alternative approaches are required. Viruses manipulate host cell biology through the expression of proteins that modulate the immune response. We hypothesized that metagenomic sequencing of viral communities would be useful to identify both known and unknown host immune proteins. To test this hypothesis, a mock human virome was generated and compared to the human proteome using tBLASTn, resulting in 36 proteins known to be involved in immunity. This same pipeline was then applied to reef-building coral, a non-model organism that currently lacks traditional molecular tools like transgenic animals, gene-editing capabilities, and in vitro cell cultures. Viromes isolated from corals and compared with the predicted coral proteome resulted in 2503 coral proteins, including many proteins involved with pathogen sensing and apoptosis. There were also 159 coral proteins predicted to be involved with coral immunity but currently lacking any functional annotation. The pipeline described here provides a novel method to rapidly predict host immune components that can be applied to virtually any system with the potential to discover novel immune proteins.

KEYWORDS:

cnidarians; comparative genomics; coral; evolution; immunity; viruses

PMID:
27581878
PMCID:
PMC5013795
DOI:
10.1098/rspb.2016.1200
[Indexed for MEDLINE]
Free PMC Article

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